Shinji X
by gunman
Summary: After a devastating battle, a nearly dead Shinji is resurrected as a razorclawed super weapon, with ferocious results. Not exactly an XMen crossover ShinjiRei pairing. Chapter 1 Edited.
1. The New Weapon X

_**SHINJI X  
**_by Gunman

Disclaimer: I do not own Shinji, the EVA universe, or any other anime with people possessing super human powers.

Author's Notes: This one has been on my computer for a while now. And as I've been working on a dozen other projects, not to mention working in general, I just recently managed to find the time and the will to finish this story. At least to the point of a first chapter.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Chapter 1  
**The New Weapon X**

"SHINJI! DON'T YOU DO ANYTHING STUPID!" Misato Katsuragi shouted through the comm. link to Unit 01 as the boy pilot continued to battle the Angel.

Inside the Geofront the Third Child of NERV was focused on a single task... saving his friend and potential love interest: Rei Ayanami.

Asuka was still in a coma following her brain-scrambling by the 15th Angel. Shinji had been delayed in trying to help his friend, who had been sent out to fight the Angel, by his father for an unknown reason. However, Shinji's sense of urgency had pushed Unit 01s synch ratio to a super high level just like during the 14th Angel attack.

Everyone remembered what had happened last time.

"EVA HAS GONE BERSERK!" Maya Ibuki shouted.

The strange glowing, snake-like Angel had tried to initiate first-level contact with Rei and her Unit 00, which was what Gendo wanted. It was all part of his plan. But his plan now had one terrible flaw in it... Shinji.

Somehow his synch rate with Unit 01 had caused him to override all commands that Gendo had tried to initiate.

The Dummy Plug System... the shut down of Unit 01... even the pressurization of the LCL inside the entry plug... all failed. It was as if Unit 01 itself was preventing NERV from trying to regain control of the biomechanical weapon.

It might have been better though, as the Angel was currently trying to painfully merge with Unit 01 after Shinji had taken the Angel out of Rei's unit. However, the pain that Shinji was feeling now was a direct result of that action.

An action that had only one recourse.

"UNIT 01 HAS INITIATED SELF-DESTRUCT MODE!" Maya screamed as she desperately tried to override the command.

"WHAT? How The Hell Did He Know Where The Damn Button Was?" Misato shouted then barking orders to Makoto and Shigeru to help Maya.

"You're Surprised?" Ritsuko shouted, trying to help her assistant, Maya, shut down the Eva. "He's Been Depressed For Weeks!"

"That Doesn't Mean..."

"COUNTDOWN INITIATED AT THIRTY SECONDS!" Shigeru shouted.

Everyone watched, helplessly, as the timer counted down.

(Rei...) the crew heard Shinji's voice through the intercom. (I'm sorry I couldn't do better than this. I love you.)

Everyone could have sworn they heard the albino girl gasp inside her Eva.

"TWENTY SECONDS!" Shigeru shouted.

(Misato... thank you... for trying your best to take care of me... like a mother...)

Tears filled the purple-haired Major's face as the countdown continued. _Shinji..._ she thought.

10, 9, 8, 7, 6, 5, 4, 3, 2, 1...

No other words were spoken, as the timer reached 0.

The blinding flash lite up the Geofront, contained within the unusually powerful AT-Field that the boy threw up around him to protect everyone he could from the blast. The fierce rumbling shook the NERV crew off their feet, their eyes covered as Unit 01 vanished.

From the bridge the reactions were mixed.

Gendo was upset. Misato and Maya were crying. Ritsuko's lip quivered. And Rei... felt tears emerge from her eyes.

_I am... crying_. Rei thought as she wiped away the moisture from her cheek. Her injuries from the Angel attack had caused her Entry Plug to eject, and Rei was watching from outside her Eva. Before now she had never known what it was to lose something. Guilt, shame, and now... love, for she had effectively lost the only who actually cared for her. _Shinji... my Shinji...-kun_. She thought as she dropped to her knees as tears flowed down her face.

Misato was the first person to notice this... and tried to connect to the Eva.

"Rei..." she whispered, "Are you... alright?"

(Major?) she whispered into the mic. (Shinji... he is... is...)

"I know, Rei. I know." she said, wanting to embrace and hug the girl, thinking that she herself needed it just as much, and that Rei had called Shinji by his first name. Not something that she would have noticed at first.

Gendo was fuming a bit at what he considered a disgustingly touching scene.

"What is the status of the Angel?" he asked, breaking the sad tension.

"Blue... blue pattern has gone silent. Pilot Ikari has... destroyed it." Maya choked back the tears.

"What about Unit 01?" he asked.

"All the readouts are negative. Magi reports that... Unit 01 has suffered... 98-percent damage." Shigeru stated in confusion. "It's like it's... virtually all gone."

Gendo growled at that.

"What about the core and Entry Plug?" Ritsuko asked.

"Uh... sensors are reading a faint power signal coming from Unit 01's S2 Engine... there's also some residual energy coming from the remains of the Entry Plug." Shigeru said.

"But.. shouldn't the plug have been ejected before it exploded?" Misato asked.

"No. All ejection controls were overridden... by Unit 01." Ritsuko explained.

The purple haired woman and the blue haired girl just cried as they heard this.

Gendo was getting upset at the weakness everyone around him possessed.

"Ritsuko." the dark man spoke.

"Sir?" the blond woman replied.

"Have the remains of Unit 01 taken back to the cages... we'll see what can be salvaged and put into the remains of Unit 03." he ordered.

"Yes, sir." Ritsuko exclaimed with some distaste.

"And we'll need to see about finding a replacement pilot, as all our pilots are now... useless." he said with conviction.

_Shinji dead... Asuka in a coma... Rei an emotional wreck_. Ritsuko thought. Though part of her was actually enjoying seeing the little doll in pain, it hurt that the source of the pain was Shinji.

Ritsuko had nothing against the boy. In fact she considered him a better person than his father.

Gendo dismissed everyone and went to his office.

Once Rei had gotten herself back to base, cleaned up and dressed in her school uniform (her only outfit really), she was met outside the locker room by Misato.

"Rei..." the purple-haired woman said.

"Major..." the bluenette girl replied.

Misato pulled Rei into a tight hug as she cried. And oddly enough... Rei didn't pull away from the woman whom she had never shaken hands with before, and was now being hugged by her.

"Come on Rei. Let's get you home." Misato said to the girl, turning away and leading Rei to the garage.

She gasped when she felt Rei's hand clutch her own. If Misato didn't know any better, she could have sworn that the girl didn't want to be alone now.

In a way... she didn't want to either. But before she could ask...

"Major?"

"Yes, Rei?"

"May I ask a favor of you?"

Under the circumstances, Misato couldn't say 'no'.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

In the large dark office of Gendo Ikari, the scheming commander and collaborating doctor were talking.

"I want Plan X up as soon as you retrieve the boy from what's left of the entry plug." he said as he sat at his desk, hands folded in front of his face.

"Plan X?" she gasped. "Are you sure?"

"You have the information concerning it, don't you?"

"Of course." she said, stuttering slightly. "But... who will you use?"

She only asked because it didn't seem as if he wanted to use Shinji, since he was dead anyway.

"What's left of the Third Child." Gendo stated.

Ritsuko gasped. "Shinji's alive?"

"Barely. I want you to get started immediately."

"But... he's your son." she said, suddenly wondering why she was trying to appeal to his humanity.

Or lack thereof.

"My son is dead. Begin Plan X as soon as you can." he said without emotion.

"Yes, sir." she said and walked out, not letting the man see her scowl of disgust.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Misato and Rei arrived at Misato's apartment, the former warmth that had once filled the dwelling obviously gone.

Misato had invited the quiet and lonely girl to her apartment, mostly because she felt she too had suffered a terrible loss like she had.

Misato had offered Rei something to eat, but was politely declined. Misato herself didn't feel like eating anything either. Her own 'cooking' felt more like an inconvenience, so she decided to drown her misery in her beer. She had lost the two most important people in her life now. The first had been Kaji, the man she had loved, and the second was Shinji, the son she always wanted.

And so she drank.

Rei on the other hand found Shinji's room, not really being in a talkative mood with the Major.

The second she stepped through the door to his room she noticed that, like Unit 01, it smelled like him. Like Shinji.

She walked over to the bed and laid down, immersing herself in the scent that was Shinji. She then noticed his SDAT sitting next to the pillow. A tear welled up inside her as she put the plugs into her ear and pressed the Play button.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

(NERV Infirmary)

Shinji's body was wheeled into the dark room, all manner of high-tech electronic device that could be conceived was around them.

Ritsuko dismissed the orderlies with a wave and leaned over the body of the Third Child.

She looked at him, running a hand through what was left of his mussed and frayed hair. His skin was burnt and cut up, his plugsuit looking like it was nearly fused to his body. His nerve endings were most likely dead and if his breathing were any more shallow, he'd have been declared dead.

Officially he was, but that mattered little to Gendo.

_Fucking bastard! He's your son!_ Ritsuko said, fighting back tears. There were no cameras in this room, but she managed to keep her composure up well. _Well... if he wants Plan X, he'll get Plan X!_ she thought as she leaned down and kissed Shinji's burnt forehead. _Yui, I've never had any love for you, and I have nothing but loathing for your husband. But your son... him, I'll save!_

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Ritsuko worked long into the night preparing the boy for the final implementations of Plan X. She had been able to use special adrenaline and booster shots to accelerate his bodies natural healing ability but also numb the pain he was under. She also had to cut off the remains of the plugsuit that was either burnt or melted off his body. A lot of the process involved making sure that there were no more foreign objects on Shinji's body as well as cleaning the wounds and such.

It was nearly three in the morning when Gendo and his hand-picked staff arrived.

"Is he ready?" Gendo asked.

"Yes, sir." a tired looking Ritsuko said. "We can safely move him to the experimentation room."

"Excellent." the grim man said and silently motioned for the orderlies to move Shinji out. He turned back to the woman. "Are you coming, doctor?"

"I've been up all night. I need coffee." Ritsuko huffed.

"Very well. Ten minutes." Gendo said and then left.

Ritsuko shot daggers at the back of his head, wishing she had real ones.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

"You are five minutes late, doctor." the unhappy Gendo said as Ritsuko walked in.

"Blame the coffee machine, sir, not me." Ritsuko complained as she went right to work.

The other techs and lab workers busied themselves with the preparations and special equipment while Gendo conferred with Ritsuko.

"So, is this plan sound?" he asked the woman.

"Yes. However, the project has never had any real success." Ritsuko explained.

"What do you mean?"

"The last known success was a man named James Howlett, back in 1955. Unfortunately another casualty of Second Impact." she continued to explain as she calibrated the special equipment that she needed for the experiment. "As you know, the Weapon X Project was originally designed by the Canadian government to create artificially enhanced super soldiers to protect their country from a variety of threats. But the project was discontinued when one of their test subjects, one Victor Creed, went crazy and killed virtually everyone in the lab. James Howlett was the only known success, but he escaped in the chaos."

"And what about Creed?"

"His enhancement eventually resulted in his death. His body couldn't handle the tremendous strain it had been put under. While it gave him incredible strength and power, it overloaded his body to the point of extreme exhaustion."

"Extreme exhaustion?"

"Yes. He burned out. Almost literally. According to the last autopsy reports all his internal organs were pushed beyond their intended capacity and limits, unable to be healed, they were liquified."

_There's a nice image._ he mentally huffed.

"Anyway, the scientists at the time speculate that James Howlett survived because of an anomaly in his physiology." Ritsuko continued.

"You're referring to his healing factor."

"Yes. A genetic mutation that was almost biblical in status."

"The reports on the project vaguely mention it."

_Really? It was only the __key__ to the project's success._ "That's what the reports indicated." she said.

"Interesting."

Then a thought struck him.

"And you suspect that the Third will not survive the process without one."

She fumed at his use of the term 'Third' as it applied to Shinji. "Yes. It would be a waste not to get this right the first time." she said.

"Trial and error are all parts of the scientific process." he said dismissively.

_Of course you would say that about your own son._ She mumbled angrily. "We don't have any other subjects, sir. And there are also time constraints to consider."

"Time, yes. We have more than you think."

"In that case..." she said then turned back to the other techs. "Listen up, people!"

The technicians gave her their full attention.

"We're going to go slowly with this, try and get it right the first time! Estimated time two-hours per stage of experiment."

"Two Hours?" Gendo gasped. "There are SIX stages to the process!"

"Yes. And I want to get each one right." Ritsuko stated.

Gendo huffed. "Very well. Notify me when the final stage is getting ready to be implemented."

"Yes, sir." she replied.

With that, Gendo left.

Ritsuko grinned internally as he left. _Now, let's do this_.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Shinji was carefully laid upon the table as the technicians gathered around him.

"Start level, Dr. Akagi?" one of the techs asked.

"Genetic mapping, level seven." she said.

"Full body then."

"That's right."

"Understood."

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Ten hours later...

The first stage of the process involved a complete genetic mapping of Shinji's body, which also included past data taken of him, involving every type of scanner and recording device they had. Every cell had to be accounted for.

The second stage of the process involved fine-tuning and locating the necessary entry points of Shinji's body for the special medical needles to be inserted. Points that had to be programmed into the computer and the mechanical needle arms, and be accurate to within a couple millimeters.

The third stage of the process involved repairing the damage to Shinji's body, first with the physical healing of cloned skin made from Shinji's DNA. A process done at the same time as the computer programming for the insertion needles.

The fourth stage of the process involved genetically altering the specific DNA strands that would give Shinji an enhanced body, specifically his bones and muscles.

The fifth stage of the process involved genetically altering the rest of Shinji's body. This included his eyesight, auditory systems, physical strength and regeneration powers.

It had been an exhausting process to prepare Shinji for the final stage of the experiment, mostly spent mapping, cleaning, repairing, and enhancing him.

Actually enhancing all of Shinji's body, not just his healing ability.

"All right, test time." Ritsuko said as she picked up a scalpel and stepped up to the boy. "Nobody breath." she said as she made a long incision into Shinji's left arm.

Everyone just stared at the boy as the long deep cut quickly vanished, the wound healing itself up, starting from where Ritsuko started to where she finished. There was nothing to indicate that there had ever been an incision. No scar, no line, nothing.

Ritsuko breathed a sigh of relief. _Bet you could have used this when you first piloted, Shinji-kun._ She thought. "All right. Artificially-enhanced healing factor functioning better than expected. We can begin the final process." she said as the techs lifted Shinji off the table and carried him over to the large glass and metal case in the center of the room.

They set him onto the metal stretcher that was suspended above it and attached a breathing apparatus to his face before lowering him into the strange liquid.

"We're ready to begin, Dr Akagi." the tech said.

"All right. Submerge Shinji into the tank." Ritsuko said.

No one noticed, or cared, that she used Shinji's name.

Just then, Gendo walked into the lab as Shinji was fully submerged into the tank.

"Akagi. How is the project coming?" Gendo said.

_Damn it! Who summoned him?_ "We're in the final stage of the process." she said, miffed that he was here.

"And the test subject?"

She glared at the man with contempt, for referring to Shinji as a 'test subject'. "Responding well."

"Then let's get this project underway."

Ritsuko nodded, knowing that her modification to the process would go unnoticed.

The original intent of the Weapon X project was to graft adamantium metal to the skeletons of a select group of individuals in order to turn them into superhuman agents. A secret strike force that no one else had.

And naturally, the stronger the bones of these agents, the stronger their physical strength and even their skin.

At least, that was their intention.

The secret to this project: Adamantium, a virtually unbreakable metal alloy artificially created by unknown scientists. Whether or not they were total geniuses or complete wacko's was never known. But the metal they created was a success. The problem was that the adamantium had to be kept at super heated temperatures in order to make it malleable and shaped into whatever they wanted. Once it cooled, however, the metal itself becomes totally unbreakable and impossible to chip, bend, break, rust or even super-heat to reforge.

However, only one person ever survived the bonding process, and that was because of his unusual and natural healing powers. All other attempts to graft the adamantium metal to other select individuals had met with horrible failures and even more horrible deaths.

To compensate, and thus save Shinji's life, Ritsuko had augmented the boy's physiology, giving him an artificially enhanced healing factor. It was hoped that this would be the key to saving his life as the process was initiated.

And if completely successful, Plan X would give them a new super weapon who would be of more use to them than Shinji had been as a pilot. Shinji's Eva was gone, so there was little point to keep Shinji around, until Gendo suggested Plan X to get some use out of the boy.

"How is the process going?" Gendo asked as the mechanical arms moved into place above Shinji.

"As well as can be expected, considering this is our FIRST test subject." Ritsuko groaned, with emphasis on 'First'.

The pair watched as Shinji was still asleep under the water, the mechanized syringes locking onto the exact entry points on his body.

"Are the straps and cuffs secure?" Ritsuko asked one of the techs.

"Yes, doctor." the tech replied.

"Those straps and cuffs are leather and titanium. They'll be the only things keeping him contained, and us safe, when the final process is initiated." she explained.

"Is it that bad?" Gendo asked.

"Unfortunately, yes. Even though Shinji's half-dead, his nerves numbed and he's teetering on death, this process is going to be extremely painful. If there's any life in him, he's going to wake up with an urgent need to scream. He'll thrash around and hopefully be unable to break free."

"You overestimate the Third Child, doctor. Even fully conscious and unhurt he would never be able to break out of plastic paper straps."

Ritsuko glared at the man, seeing him laugh at his own bad joke.

_Just wait, Gendo. If I'm right about this..._

The mechanical syringes whirred to life as they moved towards the unconscious Shinji.

Ritsuko winced as the needles were inserted into his feet, his ankles, his thighs, his hips, his spine, his rib cage, his upper arms, his lower arms, his hands, the back of his neck, and his skull.

She had seen experiments where needles were inserted into the bone and a chemical was injected. And granted that the subject was always unconscious and drugged up, but this magnitude of use was beyond anything she had ever seen. The pain of drilling into Shinji's body was enough, but the heat from the liquid metal Adamantium would have caused anyone to scream in absolute and indescribable pain.

She felt truly sorry for Shinji, and what was to happen.

Suddenly, Shinji's body jumped.

"What's happening?" Ritsuko asked.

"Adamantium bonding process is taking effect!" a technician shouted.

"Life signs weak, but stable!" another tech shouted.

"Sensors indicate adamantium process has spread to entire skeletal structure." a third tech shouted.

Shinji thrashed briefly.

"Doctor! Heart rate has just jumped!" The first tech said.

"Nervous system is firing on all levels!" The second tech said.

"Pain threshold has reached it's limits!" The third tech said.

Ritsuko looked over to Shinji in the tank, her eyes frozen as she watched him thrash violently and continuously. It looked like he was screaming.

"Activate sedatives! Double Dosage!" she ordered.

The order was carried out and the drugs were pumped through the tubes into the boy.

"No Response!" a tech shouted.

"What?" Ritsuko gasped.

"The sedatives aren't working!" a second tech shouted.

_His healing powers are negating them. Just like I thought._ Ritsuko mused.

Suddenly, Shinji exploded from the tank, the titanium cuffs and leather straps breaking like wet paper.

"Security, get in here!" Gendo ordered.

A half-dozen men in black suits stormed the room, their guns drawn.

The wires and tubes were still hanging off of Shinji as he glared angrily around the room.

"Secure him!" Gendo shouted.

The guards and the techs rushed the boy, the techs armed with emergency tazers, the guards with their guns.

Shinji's world became nothing but red, pain lanced his arms as without warning, six claws shot out from between his knuckles, three on each hand and each a foot long, his arms instinctively lashing out and impaling one of the techs and one of the guards.

Everyone in the room froze as Shinji let loose a ferocious scream and quickly shot through the air. The guards opened fire, but because Shinji was leaner and smaller than they were, hitting him was next to impossible.

His claws cut into numerous people, a count that Shinji couldn't keep if he even cared to. Screams and blood filled the room.

Shinji then saw two people standing in his path.

One a blond haired woman in a white lab coat. One a man with a brown beard and tinted glasses. He thought that they looked familiar.

The bearded man pushed the blond woman in front of him, towards Shinji himself.

_Bastard_! Ritsuko thought as she fell towards Shinji.

However, Shinji lunged forward, leaping over Ritsuko and heading straight for Gendo. The grim man turned as the boy screamed heavily, a heavy downward slash taking a chunk out of Gendo's face before he knew what happened.

The man fell to the ground as Shinji saw his way out, and took it.

Ritsuko quickly moved to Gendo, but kept her eyes on the door where Shinji had escaped.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

In another part of the world, a young girl woke up with a start. A throbbing in her head caused her to shout, unleashing a torrent of psychic force that blasted half of her furniture out of her room.

In seconds, a half-dozen other people exploded into the room. They were lead by a large man with skin that seemed to be made of steel.

"Iris? What's wrong?" Eric, the large man of steel asked.

"I'm not sure. I felt...pain." the young girl said.

"Yours?" Nancy asked, the purple-haired woman appearing by her bed.

"No. Someone else." she stopped holding her head and got up to get dressed. A fierce determined look in her eyes now. "Get the jet ready. All of you get packed. I'm sure I'm going to need your help."

"The jet?" the blond-haired Ginji asked

"Our help?" the red-haired Robin asked.

"What for?" the blue-haired Toga asked.

"And where are we going?" the blond-haired Naruto asked.

"To Japan. I'll know more when we get there." Iris said as she shimmied out of her nightgown.

"Okay. But do you want to tell us why?" Robin asked, the boys looking away from the girl.

"I sense a person in pain. Someone in Japan has been exposed to some form of genetic alteration. Experimented on. We have to find him and help him." Iris said.

"Wait, wait, wait. You felt this guy, all the way in Japan?" Naruto asked.

"Yes. I did."

The group looked at each other in shock. She turned to face them.

"Keep in mind that I found all of you the same way." she said.

The group relented.

"But why us?" Nancy asked.

"Because we are the only ones who can." she said.

"How do you know this?" Robin asked.

"I felt it. I've never felt pain or anger like this before. If we don't hurry, the situation could become serious. Deadly serious." she said as she grabbed her teddy bear.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Authors' Notes:

Hope everyone enjoyed this little first chapter of 'Shinji X'.

This is a story I've been working on for some time, but never thought it was good enough to post. Chapter One is finished, and most of Chapter Two is done. Chapter Three I think will introduce Shinji and the others to this mysterious group of individuals who are coming to help Shinji.

I'll leave it to you to figure out who is who and what powers they have.

No hints.

Also, if you want you can think of this as an X-Men crossover, though I won't be using the X-Men themselves for this.

Plus, I am also giving you this story now to tide you over while I finish up my other stories.

See you later and give me lots of reviews.


	2. Reunions and Explanations

_**SHINJI X  
**_by Gunman

Disclaimer: I do not own Eva, Weapon X, and other anime's.

Authors Notes: I've been getting a lot of reviews about the length of Shinji's claws. Just so everyone knows, They are a foot long, but there are six claws total.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Sun S Li: Guess I did miss a couple things. Sorry about that.

King of Darkness: Yes, Crazy Shinji is a lot of fun. As to your questions (Gendo's not dead, yet. I plan on having Rei and Shinji get together. There's one more Angel left. As for Naruto and Robin, I'm basically putting together a team of X-Men-like heroes.)

Wynk: I guess I should have said 'six claws that are each a foot long'

Otoole': The claws are only foot long, but there are six of them.

Ronin Katarn: Yeah, I thought that was funny for her to be serious and clutching a stuffed toy.

Anskiere: Sorry bout that. Shinji's claws are only a foot long, but there are six of them.

Neferius: Sorry! His claws are a FOOT LONG! But there are SIX of them!

King of Mana: At least you got the claw thing.

Legato Deathscythe: Sorry. But like I said before, there were six claws each a foot long!

Arus Neigh: I'm working on a Shinji/Spider Man crossover, but via a different venue than just a single character-becomes-a-hero story. And the claws on Shinji are only foot long, but there are six of them!

Him0nky2012: Jeez you're brutal. First of all, yes I made a mistake about the Angel. Sorry. As for Asuka, this is a fanfic, which means that I can put her into a coma whenever I want. And I don't see anything wrong with the capitalizations, even though I fixed them. And who's side are you on? Gendo is a bastard. Plain and simple. He's the ideal villain for this anime. I mean come on! The guy abandoned his own son, he's screwing women he works with just because he's 'the commander', he sent Rei1 to torment Naoko Akagi which lead to her suicide, he isolated Rei2 from the world, he's involved in dozens of illegal activities such as cloning, accessory to genocide, his part in Second Impact, he ordered the Dummy Plug activated that nearly killed Toji Suzuhara using Shinji as the 'hands', and you'd know he'd willingly kill, torture, blackmail, 'suicide', and rape anyone to get what he wanted. There is little humanity left in the man, so don't play Devil's Advocate with me.

And if I wanted to write an X-Men story, I would have written an X-Men story. And what do you mean that Eva and X-Men don't have a lot in common? Maybe not in-character, but you could easily put several of the Eva crew into X-Men positions. As it is, only Shinji and probably Rei are going to be along the same line as the X-Men, what with the other characters I've brought in.

Jonakhensu: You're right about Shinji seeking out his home, and yes, Shinji will be first on Gendo's kill list when he wakes up.

Shinjithegoodsharer: Sorry to disappoint you. But this is a Shinji-Rei fic. No having his way with Ritsuko.

Mangafreak7793: I'll put more details into each character in the last half of this story.

Dartz-IRL: Sorry, I'm a little scatterbrained when it comes to things, so I tend to get sidetracked a lot.

Dennisud: The characters in this are sort of an alternate anime-style X-Men team. Rei's powers will be read by my readers in future chapters.

anynomus: Don't worry, I'll post a list of who-is-like-who at the end of this chapter.

Dragonmage182: You were one of the few people to get that Shinji's claws were only a foot long and six in number.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Chapter 2  
**Reunions and Explanations**

Shinji scrambled through the dark hallways of NERV, each twist and turn confusing the boy more as he ran. His mind was in a jumble from everything that had happened. Not that he remembered all the details.

He remembered pain. He remembered men in dark suits trying to hurt him. He remembered a woman with yellow hair pushed towards him. She didn't seem like a threat so he leapt past her to attack the man in the beard, the one who felt like a threat.

He felt pain in his hands as he tried to stop the unfathomable torment that caused him to lash out at everything around him in an attempt to even dull the pain.

Pain filled his mind, along with other images as well.

A woman with purple hair who always smelled like beer. A girl with short blue hair and red eyes who only smiled once. A swimming bird.

An apartment.

Shinji paused for a second, turned around, and ran towards the nearest exit.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

It was just past three o'clock in the afternoon.

School hadn't let out yet and most people were working, so they failed to see the frantic child speed through the city, draped in wires and wearing what looked like a pair of black biker shorts, and make his way back to an apartment building he didn't recognize, but knew that he knew it.

But he wasn't sure how.

Groggily climbing the stairs he made his way to the seventh floor and hauled himself over to the door at the middle corner of the building. The electronic keypad next to the door spoke to Shinji as he typed in the code.

_What? How did I know..._ he thought as the door slid open.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Rei sighed as she hit the replay button again on Shinji's SDAT. She hadn't really left Shinji's bed since the incident. She shed another tear as she thought about Shinji.

_Shinji-kun... when will you come home to..._ her eyes popped wide open as a familiar feeling went up her spine. She sat up in bed and looked to the door. _It cannot be..._

Rei emerged from the bedroom and ran to the front door, pausing when she saw the tired looking form of one Shinji Ikari standing before her. Dressed in black shorts and with some wires hanging off of him, he looked ready to pass out.

"Shinji-kun?" she asked.

Shinji froze and stared at the blue-haired girl before him. He stared at her with some confusion. His eyes couldn't place her, but his mind knew her image.

"Who are you?" he asked.

Rei tilted her head to the side. "You do not know me?"

"...no..." he said, continuing to stare. "I...know you...but I don't...remember..."

Meanwhile in the kitchen, Misato was slowly waking up from her half-drunk stupor when she heard voices. (Not those kind)

_What the... is Rei up?_ She wondered as she groggily got up and went to investigate, freezing in the hallway as she stared at Rei and...

"Shinji-Kun?" she gasped loudly, not noticing PenPen waddle up behind her in curiosity.

Startled by her sudden appearance, and the overwhelming stench of beer, Shinji reacted on instinct. Six claws suddenly shot out from his hands at the woman, the penguin scattering away in fear.

Fortunately she was a couple meters away from him when he did that.

"What the..." Misato gasped in shock, but Rei just stared at him, clearly confused at this strange new development. But she was more curious and concerned than fearful at where Shinji had acquired his new implements.

Misato looked at Shinji, her beer buzz clearly wearing off an her concern for Shinji took hold. She stepped cautiously towards the boy.

"Shinji-kun?" she walked closer to him.

"Who... are you?" he asked weakly, starting to waver as his claws slowly retracted into his hands, his eyes getting heavy.

Out of concern, Misato moved towards him, her hands outstretched to catch him if he fell.

"Shinji, do you remember me?" she asked softly.

His claws fully retracted, Shinji stared at the woman.

"You...drink... too much..." he said as he passed out, falling forward as Misato lunged and caught him in her arms. He passed out fully, head on her shoulders, as the purple-haired woman hugged the boy tightly while tears fell down onto Shinji's shoulders.

Rei gave her a strange look, which was her equivalent of looking jealous.

However, Misato didn't notice (not that she would have) as she was just glad that her Shinji was back. And whatever was wrong with him, she swore she would be there for him.

"Rei, help me get him into his room." Misato said after several minutes of motherly embracing, the blue-haired girl nodding.

The pair didn't fully understand how Shinji had become so heavy all of a sudden. He felt at least twice as heavy as he had been in the past. It took some effort to get him back into his room and onto his bed.

"Rei, I have to get to NERV and find out what's happened to Shinji." Misato said.

"Of course. I will stay with him." Rei volunteered.

"Will you be alright?" the woman asked.

"I have missed him." the girl assured.

Misato actually smiled at that.

"Alright. You... comfort him. Meanwhile... I'm gonna get to the bottom of this." she said as she went to get changed.

"Major!" Rei suddenly spoke up.

"Yeah?" she asked, turning back to the girl.

"Perhaps it would be wise not to mention that Shinji-kun is here."

"Huh? Why?" she asked.

Rei cocked her head to the side, as if confused by the obviousness of such a question. She turned back to the unconscious boy.

"Something has happened to Shinji-kun. Something that is possibly of NERV's doing. If they learn he is here..." Rei started to explain.

"Right. Ask about Shinji, but tell them nothing." Misato sum-upped.

"Correct." the girl said as she turned her attention back to Shinji.

_Smart girl_. Misato grinned as she headed to her room. _Huh. Where did PenPen get to?_

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Misato spent the latter part of the day trying to find out about Shinji's condition from Ritsuko, telling the blond scientist that she didn't believe Shinji was dead. She also wondered where the commander is at this time. And Ritsuko kept dodging the questions.

While Misato continued to get the run around at NERV, Rei continued to comfort Shinji in the only way she thought possible.

Sleeping with him.

She removed her clothes, down to her white cotton panties and bra, then removed the wires that were still hanging on his body, before sliding into the single bed and against the boy.

_He looks so peaceful when he sleeps._ Rei thought as she brushed a stray lock of hair out of his eyes. _But what has happened to you I wonder. I thought you were dead. But you have returned. No, not all of you has returned. Your memory has faded, and in place_, she paused, running her fingers over Shinji's hand, _you have gained something else. _

Saddled up against the boy, Rei couldn't help but come into close contact with the Third Child. However, it was this gentle stroking of the hand that caused Shinji to stir.

He blinked his eyes open and stared at the girl. "Hello." he said.

"Hello." she replied back.

"Who... are you?" he asked.

"You do not know who I am?" she asked, slightly hurt.

"Uh... no. I don't." he said, though by the look in his eyes he was trying to remember.

Rei looked away for a few seconds, before turning to him, trying to act upset. But in fact she was smiling. (The typical Rei-smile which is so gentle most people don't see it when it happens)

It was then that Rei did the most out of character thing she had ever done.

"I am Rei Ayanami. I am Your Girlfriend." she said.

Shinji's eyes gently lit up as he stared at the girl, recognizing the term but not the usage.

"My.. Girlfriend?" he gasped.

"Yes. You said that you loved me, before your... accident." she explained.

_Accident? Is that why I don't remember her?_ He thought. _I said that I love her? _

He looked at Rei.

_Well... she is pretty. And kind. Maybe I did say that_. He thought. "Rei?" he asked.

"Yes?"

"Did we ever... kiss?" he asked, blushing at the question.

Rei leaned in and tenderly pressed her lips to Shinji's.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

"How is he?" Ritsuko Akagi asked the doctor as she stared at the heavily bandaged face of Gendo Ikari.

"The wounds are fairly deep. But I have to say, it's a miracle he survived." the glasses-wearing doctor stated.

_Miracle? Dumb luck. Maybe I should have made Shinji's claws longer_. Ritsuko thought. "How bad are his injuries.

"The slash marks go from the upper right side of his face to the lower left. His left eye is gone, his nose is literally cut in half, and his jaw was severed at the chin. We managed to reset it, but he might need a metal replacement." the doctor explained.

Ritsuko grinned a little, not that Gendo, or the doctor, could see. _And Frankenstein is born. _

"We're not sure how, but he's refused to talk. At first we thought his vocal chords had been severed, but there was nothing to indicate they were damaged by whatever animal attacked him. But I've never seen incisions like this from any animal. What did attack him, Dr Akagi?" he asked curiously.

"For now, that's classified." she replied. _Not talking from the physical wounds. Psychological perhaps?_ She mentally grinned.

"Of course." the doctor relented. "As I said, he's refusing to talk, but I don't think the trouble is the physical injuries. However, a complete facial restructuring would take several months at least. Maybe a year."

_He's not talking at least. Good. I could use some peace and quite around here._ Ritsuko thought. "Alright. Keep me informed of his progress."

"Yes, Dr Akagi."

Ritsuko exited the hospital room, her mind working on what excuse to give Misato when she saw her tonight.

Misato hadn't been able to get anything out of Ritsuko when she first got into NERV, even on the whereabouts of the commander, so she eventually pestered the blond scientist into meeting her later tonight for dinner at her apartment. And Ritsuko knew better than to stand the purple-haired Major up, otherwise she'd hunt her down and then have her little talk.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

While Misato was doing her delicate inquisition, Rei was quickly becoming a normal teenager.

And by normal, that meant she was making out with her boyfriend.

Both Shinji and Rei spent the whole afternoon kissing and cuddling while lying in bed, the girl trying to jog the boy's memories of his life. Not a lot came back to him, except the sad feeling he got of his mother when Rei let him listen to his SDAT recordings.

It was a sad memory, but a memory he thanked her for.

Rei also found that she liked kissing her Shinji-kun, as she called him. The close physical contact, the warmth building up inside her, her rapid heartbeat, the feel of his hands as they encircled her body to hold her close.

She especially liked laying on top of him like a blanket when they kissed.

Misato eventually came home and found the pair snuggled closely in bed. She decided not to tease them, just giving them much needed privacy as they both looked amazingly happy. She did tell them that Ritsuko was coming over for dinner later, however.

When Ritsuko finally arrived at around 8 o'clock, she was met at the door by Rei Ayanami.

"Hello, Dr. Akagi." the girl said.

"Rei." the doctor replied.

Dinner was rather simple, since Misato couldn't cook, as Ritsuko knew this was mostly a question-and-answer dinner. The pair were in the kitchen, Rei declining to join them, not that Ritsuko thought that was unusual. She also wondered where PenPen was.

"Ritsuko, I need to talk to you about Shinji." Misato said, getting right to the point.

(Sigh) "First of all, Misato, you were right about Shinji. He is alive, but barely. He's in the intensive care unit, teetering on the brink of death. No one is allowed to see him until he's recuperated." Ritsuko lied to her friend, mentally adding: _And found_.

Misato only nodded, looking unimpressed.

"And there's nothing else you can tell me?" Misato asked.

"I wish there was. Sorry." Ritsuko replied as she continued to eat her questionable meal.

"I see. So, what do you think about all this..." Misato said, cocking her head to the side to talk to the person standing behind Ritsuko. "..Shinji?"

Ritsuko's blood turned cold. She had almost expected Misato to be talking to Rei, or her big mooch of a penguin. She did it often enough. She heard a faint growl behind her, which confirmed her fear and suspicion. Why hadn't she considered that Shinji might come here? She stood up and turned around to see a very pissed off Shinji Ikari just glaring at her.

"Teetering on the brink of death? Looks like he's about to administer it." Misato said calmly.

A soft growl emanated from his snarling lips as he suddenly dove towards her, knocking her across the table and onto the floor, pinning her down with his left hand on her throat. His right hand was poised over her face, his razor sharp claws jutting out and stopping just an inch from her eyes.

"TALK!" he growled. "WHY DID YOU DO THIS TO ME? WHY?"

"What... makes you think I..." she weakly choked.

"I remember seeing you! When I escaped!" he growled, vague images coming back to him the second he saw the blond woman. "NOW TELL ME WHY!"

"I...had no choice...the commander..." she groaned under his grip.

"WHAT ABOUT THE COMMANDER? YOU DID THIS FOR HIM?"

"Shinji, let her throat go." Misato said calmly. "She can't talk if you strangle her."

Shinji released her throat, but his other hand remained poised to strike her. Ritsuko realized that if she didn't give him the truth, he'd kill her.

Worse, he'd continue to think it was her fault.

"The commander ordered me to enhance Shinji after his last battle with the 16th Angel that left him nearly dead. Figuring to make him some use after the loss of Unit 01." Ritsuko explained.

Shinji's expression softened as Rei moved up to him, trying to ease his anger as she placed a hand on his shoulder. Ritsuko continued to talk.

"We used a scientific method from old military research to enhance Shinji's physical body, bonding his skeleton with a virtually indestructible metal called adamantium."

Misato gasped. "Are you crazy? No human being could survive that!"

"True. But Shinji's nerve-endings were virtually all killed off, so he wouldn't have felt anything. However, for added insurance, we had to enhance him, using genetic augmentation to give him a superhuman healing factor that constantly repairs and maintains his body."

Shinji finally moved off of Ritsuko with Rei right by his side, his claw retracting into his arm.

"I killed people." he finally said, those memories coming back to him as well.

"Yes, you did. Seven Section 2 agents, two of our techs, and you gave Commander Ikari a very nasty three-clawed scar across his face." she said with a mild smirk.

"So that's what happened to him." Misato mused.

"I'm a freak. A monster." Shinji whispered.

"No, you are not." Rei said as she hugged his arm, comfortingly.

Ritsuko noticed this, a tinge of jealously going through her. _When did they get so close?_

"What about his claws?" Misato asked the scientist.

"An unforseen side-effect of the bonding process. Somehow, you're able to project razor sharp adamantium claws from your hands. It's something we didn't know about, or take into consideration. Nor your ferocity when you escaped." Ritsuko said to Shinji, but answering Misato.

Of course Ritsuko was lying about that part.

The adamantium had bonded to the six bone shards that Ritsuko had implanted into Shinji's hands when she had Shinji alone in her office. She had the equipment brought in secret and implanted the shards, cloned awhile back from Shinji's own genetics, into Shinji's hands while he was half-dead.

No one knew Shinji's biology better than her, and even Gendo never paid attention to the medical reports she submitted. As with the old Weapon X program James Howlett had adamantium bonded to his skeleton, which also bonded to the additional bone shards that were already in his arms, giving him razor sharp metallic claws. Since Shinji didn't possess claws, Ritsuko had added them, his new regeneration powers bonding the extra bones to his muscles allowing him to control them with ease.

"Why did you do this to him, Ritsuko?" Misato asked, clearly upset at this whole event.

"Because it was the only way to save him!" the blond scientist argued.

"Save him?" she gasped.

"It was Gendo's idea to initiate Plan X. If I hadn't agreed to do it, he'd have found someone else who would have, and Shinji would have died." Ritsuko explained. "I made sure he lived."

Misato fumed. "I see."

"I am not familiar with this Plan X." Rei asked.

"It's a reference to an old military project called 'Weapon X'." Ritsuko replied.

"Sound's like a comic book." Misato brooded grimly, still upset.

"You're not far off." the blond muttered.

"What?"

"The original intention of the project was to create agents with superhuman abilities. The project had dozens of test subjects, but only one success. A man named James Howlett. And he only survived because of his anomalous healing factor."

"Anomoloo-what?"

"His cellular regeneration capabilities, his ability to heal, were beyond anything anyone could have imagined. They were almost... biblical." she explained.

"Biblical. Riiiiight." then a thought struck Misato. "Wait. Does that mean that... Shinji..."

"No. In order for Shinji to survive the process, I had to artificially enhance his own healing abilities. Even with Shinji's nerves numbed and his body half-dead, it was the only way he could have survived this whole process."

Granted Ritsuko had mentioned the genetic augmentation, but Misato was still stunned by all this to think clearly.

"Go on." Misato said.

"Anyway, the bonding process was successful, but it had to be altered." Ritsuko explained.

"Altered?" Misato queried.

"The plan was to surgically graft an indestructible metal called adamantium to Shinji's skeleton. But with Shinji still growing, this would have caused some rather... inconvenient side effects later on."

"Side effects?" Misato asked, not getting Ritsuko's subtle meaning.

"His body would have kept growing to adulthood, but his bones would be solid metal. And as I'm sure you know by now, metal doesn't grow."

Misato seemed to understand. "Right, an adult with a kid's skeleton. Very inconvenient. Go on."

"I didn't have a lot of time to test it, but I managed to successfully rework the adamantium formula to make it into an organic metal."

"Organic metal? You know how... conflicting that sounds?" the purple-haired woman asked.

"Yes, but there wasn't a choice. Shinji had been inconvenienced by all this since the explosion, but since I couldn't stop it, I had to go another way."

"Doesn't sound like the commander had any plans for Shinji to live past this year."

"Not really, no. But thanks to me, only the claws in his arms are now strictly non-organic metal. The rest of his metal-laced skeleton is virtually indestructible, but will continue to grow along with him."

"So... you altered Shinji's body, you altered the adamantium process, and ultimately altered the plan the commander set down." Misato surmised.

"Yes." Ritsuko nodded.

"And the metal in his bones will grow along with him." Rei said.

"Exactly."

"Wow, Ritz, you really are a genius." Misato said, truly impressed.

"Thanks."

"But I'm still PISSED at you!" she shouted, her mood turning sour once again.

"And you have every right to be. I didn't want to do this, Misato, but if I didn't, someone else would have and Shinji surely would have died."

"The lesser of two evils." Rei stated.

"Yes."

"It's still **evil**, Ritz!" Misato spat.

"I'm sorry! But like I said... if I didn't do this, Shinji would have died."

"Yeah. I know." she sighed.

"I don't apologize for what I've done. I don't ask for you to forgive me, but what I do want is for you to understand that I wanted Shinji to live." Ritsuko said.

"Why?" Rei asked.

"Because I like him a lot better than his father." Ritsuko explained.

All things considered, Misato and Rei seemed to accept that.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Halfway across the world, a high-tech looking jet plane flew through the air. It's passengers anxious.

"Are we there yet?" Naruto whined.

"Quite whining, blondie!" Sakura stated as she continued to pilot the stealth jet.

Sakura herself had been in the hanger when Iris's powers went off, using a rivet gun to install some new panel's onto the jet, so she never heard anything. She was about to call it a night when Iris and the whole team showed up with an important mission. She groaned, but got out of her jumpsuit and grabbed her already made travel bag.

"You should be lucky I got the Blackbird X-7 fixed when I did."

"Despite your need for sleep?" Robin asked.

"A little energy drink and I'm good to go." Sakura said. "Especially since none of you have had a full lesson in flying this thing."

"Well we would have if you didn't keep trying to upgrade this thing." Ginji stated.

"Clam it, you overgrown bug zapper!" she spat.

"Now children..." Nancy said.

While the unique group of individuals talked, Iris hugged her teddy bear and looked out the window.

_The pain has stopped, but I feel something else has happened_. She thought. _Something... missing. And something else draws near_. "We have to hurry!" she suddenly spoke up.

"After burners to full!" Sakura said as she hit the thrusters.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Author's Notes:

Here's chapter 2 of my latest superhero story, and I hope everyone enjoys it.

Sorry this update is late in coming, but aside from working on my other projects, I've also been working a full week. No day off. Not much time for anything else.

Also, since all of you wanted to know who was who, so here you go.

**Characters**

Iris Chateaubriand-telepathy and teleportation. I put her in as a sort of 'Professor X' of this world as she is quite mature. She is from Sakura Taisen.

Eric Elric-metallic body, super strength. Supposed to be the descendant of Edward Elric, the Full Metal Alchemist. I put him in as the 'Colossus' of this world.

Nancy Makuhari-phasing powers, from the Read or Die movie. Supposed to be the 'Shadowcat' of this world.

Ginji Amano-electrical power. The retrieval expert from GetBackers who I put in the place of 'Berserker' from the X-Men Evolution series.

Robin Sena-fire powered craft user from Witch Hunter Robin. I basically put her in as 'Firestar', minus the flying powers, who briefly served with the X-Men years ago. Another reference is 'Magma', also from the X-Men Evolution series.

Toga Takuji-reborn Sonic the hedgehog, super speed. Even though Toga has no super powers in the Gravion anime, he does have blue hair and so does Sonic. And I know I'm stretching this idea, from the Eva story 'Speed', but come on, every team needs a speed guy.

Sakura Kakei-telekinesis. Also from GetBackers, who I chose to have in place of 'Jean Grey'. Even though her telekinetic powers only worked when she touches things, I decided to upgrade her.

Naruto Uzumaki-super duplication. I chose to use him as the counterpart to 'Multiple Man'. Also in this world he's not a ninja, but he can still fight like one.

As for Shinji and Rei?

Shinji Ikari-claws, healing, strength. Basically I made him 'Wolverine'.

Rei Ayanami-force field powers, which makes her a lot like Dr Cecilia Reyes who briefly served with the X-Men.

Anyway, this was rather fun to write. But I have little idea where this is actually going. Any suggestions would be welcome at this point.

Here's hoping everyone sends me good reviews.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

OMAKE 1

_Just wait, Gendo. If I'm right about this..._ Ritsuko thought as the mechanical syringes whirred to life and moved towards the unconscious Shinji.

Ritsuko winced as the needles were inserted into his feet, his ankles, his thighs, his hips, his spine, his rib cage, his upper arms, his lower arms, his hands, the back of his neck, and his skull.

She had seen experiments where needles were inserted into the bone and a chemical was injected. And granted that the subject was always unconscious and drugged up, but this magnitude of use was beyond anything she had ever seen.

She felt truly sorry for Shinji, and what was to happen.

Suddenly, Shinji's body jumped.

"What's happening?" Ritsuko asked.

"Adamantium bonding process is taking effect!" a technician shouted.

"Life signs weak, but stable!" another tech shouted.

"Sensors indicate adamantium process has spread to entire skeletal structure." a third tech shouted.

Shinji thrashed briefly.

"Doctor! Heart rate has just jumped!"

"Nervous system is firing on all levels!"

"Pain threshold has reached it's limits.

Ritsuko looked over to Shinji in the tank, her eyes frozen as she watched him thrash violently and continuously. It looked like he was screaming.

"Activate sedatives! Double Dosage!" she ordered.

The order was carried out and the drugs were pumped through the tubes into the boy.

"No Response!" a tech shouted.

"The sedatives aren't working!" another tech shouted.

"Not For Shinji!" Ritsuko shouted. "I Meant For Me!"

"What?"

"You think I want to be conscious when he gets loose? DRUG ME NOW!" she shouted as she exposed her arm to the tech.

"Uh.. right." he said, injecting her, and hoping there was enough for himself.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

OMAKE 2

His claws cut into numerous people, a count that Shinji couldn't keep if he even cared to. Screams and blood filled the room.

Shinji then saw two people standing in his path.

One a blond haired woman in a white lab coat. One a man with a brown beard and tinted glasses. He thought that they looked familiar.

The bearded man pushed the blond woman in front of him, towards Shinji himself.

_Bastard_! Ritsuko thought as she fell towards Shinji.

However, Shinji stared at the blond woman for a few seconds before he dove for her. He slashed and sliced at the blond woman, moving around her body with incredible speed and agility. Within a few seconds he stopped and moved back from the woman.

Ritsuko looked at her body and gasped, not seeing any cuts or slashes on her skin.

She quickly understood why as her clothes suddenly turned to shreds and fell off her body, leaving her in nothing but her panties.

"OH!" she gasped as she covered her breasts, her bra also in pieces.

"Shinji like!" the boy growled as he leaped forward, grabbing Ritsuko and tossing her over his shoulder before running out of the room.

Gendo wasn't sure he was lucky to be alive, or upset that his son had stolen Ritsuko. (Not that he really seemed to care)


	3. Assassin X

_**SHINJI X  
**_by Gunman

Disclaimer: I do not own Eva, Weapon X, Sakura Taisen, FMA, R.O.D., Getbackers, Witch Hunter Robin, Sonic the Hedgehog, Gravion, Naruto, or anything related to the X-Men.

Summary: Shinji and company encounter the mysterious Iris Chateaubriand and her team while Gendo plans to unleash the deadly Assassin X on the failed Weapon X.

Author's Notes: This story has been on the back burner for several months. I hadn't bothered to update it for a while, until I recently received an email from a friend requesting that he'd like to see it updated. Using an idea from some of my other reviewers I came up with a pretty good subject matter for this chapter.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Chapter 3  
**Assassin X**

(Ikari Hospital Room, late night)

Fuyutsuki stood in the room with Gendo sitting in his bed, a laptop computer turned on and facing him on a small serving table.

"You wanted to see me, Ikari?" the older man asked.

Gendo, still unable to talk, typed on the laptop.

(I WANT YOU TO INITIATE 'PROJECT: ASSASSIN X') the message said.

Fuyutsuki paled. He had only a basic understanding of that project.

"Are you sure, Ikari?" the older man asked.

Gendo typed again.

(I WANT HIM DEAD!)

Fuyutsuki grimaced. He knew that this order was coming from a man who had been attacked and hurt. He was doing this for personal vengeance, because of a project he had initiated. Not that responsibility was high on his list of priorities.

"And... do we have a candidate?" Fuyutsuki asked.

Gendo thought for a minute, and typed again.

(THE GIRL)

"Girl? You mean..."

Gendo typed again.

(SOHRYU!)

Fuyutsuki sighed. He figured that it would be her. Of all the people he could think of to go after Shinji, _she_ was the most logical choice.

"She's still in a coma." he said.

Gendo typed.

(USE IT!)

Fuyutsuki grimaced at the redheaded girl being referred to as an 'It'.

"I'll see to it personally." he said before walking out.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

(Emergency Medical Facility, NERV, an hour later)

"Are you sure about this, sir?" the tech said as the still unconscious Asuka was wheeled into the specially made operations room.

"No. But it's Ikari's orders." Fuyutsuki said. "I'll be assisting in this."

"Uh... understood, sir."

Fuyutsuki paused for a few seconds, gently brushing his hand over Asuka's head. A tear almost came to his eye at what he was about to do.

_I can't do this! But... if I don't, Ikari will replace me with someone who will not be so... concerned with Asuka's plight. But if I do this, Asuka will not be the same. She will be a lethal killing machine without any form of life or humor or... humor. Wait! That just might work._ He thought with a smile.

"Sir? Are we ready to begin?" the tech said.

"Bring me the Deadpool Files." he said.

"What?"

"The Deadpool Files! Bring them to me at once!" Fuyutsuki repeated.

"Uh... are you sure?"

"Yes."

(An hour later...)

_Hmm... this might work_. Fuyutsuki thought as he reviewed the file. He turned back to the technicians who had been waiting patiently. "Alright, gentlemen! Here's what we're going to do. We're going to make a change to Project: Assassin X."

"Uh... a change, sir?"

"Yes."

"But, sir, we have a specific procedure and agenda to follow."

"I'm aware of that."

"The commander will be upset if there is any change to the..."

"Ikari won't be disappointed with this change, and it will not deviate from the original plan. Ikari wants an assassin, and he'll get an assassin."

The group of techs looked at each other.

"As you are all aware, Project: Assassin X was designed to counteract Project: Weapon X, or Plan X as Ikari called it, in case the weapon ever got out of control. Obviously it did. Our subject for this was Shinji Ikari, who was nearly killed in his last battle with the Angels. Our subject matter for this new project is Asuka Langley Sohryu. While we are going to use her for this, I think you'll agree that the project will fail if the subject dies."

The group of techs nodded in agreement.

"Therefore we are going to utilize some special procedures that will ensure that Ms Sohryu survives and so that the project goes forward." he explained. "Here's what we're going to do."

HHHHHHHHHHHHHHHHHHHHHHHHHHH

(Blackbird X-7, early morning)

Iris and her team were over the Japanese coast, most of them half asleep from the trip.

"We're here." Sakura said to the group.

"Good. Continue on to Tokyo-3." Iris said, hugging her teddy bear.

"So... who or what are we looking for?" Eric asked.

"His name is Shinji. Shinji Ikari." she said.

"WHAT?" Naruto shouted, suddenly awake. "THE Shinji Ikari? The Evangelion pilot?" he gasped.

"You know him?" Nancy asked.

"I've heard of him! Member of a top secret UN Sanctioned agency called NERV. The only male Evangelion pilot. He's gone up against virtually all of the Angels that have been attacking this country!"

"Wait! If this guy is part of a top secret agency, how do you know so much about him?" Ginji asked.

"A webpage hosted by a computer geek named Kensuke Aida. He's really the only one who knows about this thing." Naruto said.

"He must be pretty good if the government hasn't shut him down yet." Robin said.

"ETA to Tokyo-3, 27-minutes." Sakura said.

"Alright. Everyone... prepare to meet your newest teammate." Iris said.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

(Katsuragi/Ikari/Ayanami Apartment, mid-morning)

"How's he doing?" Ritsuko asked as she sipped her coffee.

"Better." Misato said as she grabbed a beer from her fridge. "Better than me."

"I understand you're still upset about this."

"I should kill you, Commander Ikari, and everyone left that Shinji didn't kill when he escaped." Misato grumbled as she slammed her beer.

Ritsuko looked at her friend, not saying a word. It was exactly the reaction she expected. Though she was glad Misato didn't have her gun on her. In her drunken state, she would have done exactly what she said she was going to do. Still, the fact that she was still alive come morning was a good sign.

(Shinji's room)

Shinji and Rei were still asleep in his room, the blue-haired girl hugging Shinji close while he slept. Rei was the first to awaken and was pleased to note that Shinji had his arms around her as well. It was as if he was drawing comfort from her, which she didn't seem to mind.

"Rei-chan?" Shinji asked softly.

"Good morning, Shinji-kun." she whispered back.

She nuzzled his cheek with her nose as she buried her head into his neck.

He smiled as he pulled her in close to him.

His memories still hadn't returned, but what he felt were real enough.

_This girl... is special to me. I can feel it. I can't remember how or why... but I just know_. He thought as he held her. _She smells nice... like vanilla. _

(Back in the kitchen.)

"I'd still like to examine Shinji's claws." Ritsuko said.

"Can't you leave it alone, woman?" Misato slurred. "I mean, YOU gave him those claws, why would you want to examine them further?"

"Scientific curiosity."

"He's not a science project Ritsuko, and you're racking up another reason for me to kill you."

Suddenly, there was a knock on the door.

"I'll get it. Shinji's still sleeping." Misato said, wanting to get away from Ritsuko as well.

Once she reached the door and opened it, she froze when she saw a young girl holding a teddy bear and seven other people standing behind her.

"Uh... can I help you?" Misato asked.

"I believe you can." the girl said. "We're here to see Shinji."

"And... for what purpose, may I ask?" she asked suspiciously.

The girl grinned. "You are suspicious of us, aren't you?"

Misato glared at the girl, who apparently fancied herself the leader of this group, as she was doing the talking.

"Whatever makes you think that?" Misato asked.

"Well, for one thing, I suppose you could call me the leader of this group." the girl said.

Misato gasped.

"And for another, we are here to help Shinji." she said.

"Help him? How?" Misato asked.

"Misato? What's going on?" Ritsuko said.

"Uh... we've got company." Misato said.

"What do they want?" the blond asked.

"Shinji." the purple-haired woman said.

Ritsuko looked at her friend in confusion

"As I said, Ms Katsuragi, we are here to help Shinji." Iris said.

"Hey! How did you know my name?" Misato gasped.

"I think that introductions would be best when all have assembled." Iris said as she suddenly vanished into thin air.

"What The..." Ritsuko started to say.

"Where did she..." Misato gasped, looking around.

"Yeah, that's what we thought when we first met Iris." Naruto said.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

(Shinji's Room)

Iris teleported herself into the bedroom of Shinji Ikari and Rei Ayanami, only to find the pair half-dressed and in bed.

"Oh my!" she gasped, holding her bear. "I guess I should have knocked."

"Who are you?" Shinji asked.

"And how did you get in here?" Rei asked.

"My name is Iris Chateaubriand. And I am here to help you." the girl said.

Shinji and Rei looked at each other, but didn't say anything.

"Please get dressed and come into the living room. It is very important." she said before teleporting out.

The pair looked confused, and annoyed, but got up, got dressed and exit the bedroom to come face to face with a young girl and her entourage.

Shinji's senses went wild as his claws pop out.

Naruto grinned. "You _must_ be Shinji."

"We've heard a lot about you." Sakura said.

"Who are you?" Shinji asked.

"I'm Naruto Uzumaki." the blond boy in the orange outfit said.

"I'm Sakura Kakei." the purplish haired young woman said.

"I'm Robin Sena." the redheaded girl said.

"I'm Toga Takuji." the blue-haired boy said.

"I'm Nancy Makuhari." the dark-haired woman said.

"I'm Ginji Amano." the taller blond haired boy said.

"I'm Eric Elric." the dark-haired young man said.

"I am Iris Chateaubriand, and this is Jean-Paul." she said as she held up her bear.

_What a strange child_. Rei thought.

"Not as strange as you, blue girl." Iris said, causing Rei to blink.

"You... can read my thought?" she asked.

"Yes. But I am not the only one with special powers." she smirked as she looked at Shinji and then at her companions.

Misato and Ritsuko seemed to get the hint.

"I take it this is going to take a long time to explain?" Ritsuko asked.

"I'll make the coffee." Misato said. _And break out the wine coolers._

HHHHHHHHHHHHHHHHHHHHHHHHHHH

(NERV Secret Medical Facility, late morning)

After hours of work the subject was resting peacefully. Or as much as possible considering what had been done to her.

"How is she doing?" Fuyutsuki asked.

"All things considered... good." the head tech said.

"Excellent." the older man said.

"She'll be ready for deployment within 24 hours. Once she wakes up." the man said.

"And the mental programming?" Fuyutsuki asked.

"Implemented as ordered." the head-tech said.

"Good. I need to inform Ikari about this." the sub-commander said as he turned and walked out.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

(Commander Ikari's Room)

Gendo looked up, seeing the older man, then turned back to his laptop and typed.

(STATUS)

"Project Assassin X has been completed. She'll be ready to mobilize within 24-hours." Fuyutsuki said.

Gendo typed again.

(AND HAVE YOU LOCATED THE BASTARD?)

"No. We're running down all leads. But considering we're using Asuka, it might be better to let her run free. She might instinctively know where to find him."

Ikari grimaced at that then typed again.

(THAT'S NOT A GUARANTEE)

"It's all I have right now." Fuyutsuki said.

Ikari typed again. (VERY WELL.)

"SEELE has been asking questions. They want to know what the delay is with the Instrumentality Project."

Ikari grimaced and typed again.

(THEY CAN WAIT!)

_You can say that. I have to deal with them_. He thought.

Ikari typed again.

(DEPLOY ASSASSIN X AS SOON AS POSSIBLE)

"Understood."

HHHHHHHHHHHHHHHHHHHHHHHHHHH

(Katsuragi/Ikari/Ayanami apartment, the next day)

The last twenty-four hours had been rather tumulus to the group.

Misato and Ritsuko were stunned when they found out that Iris and her team all possessed special powers like Shinji.

Aside from her ability to teleport, Iris possessed the power to read minds, but also to awaken the latent powers of others. Of course, it could only be used on teenagers, which mean that Misato and Ritsuko were out of luck.

Naruto possessed the ability to duplicate himself up to at least forty people. He also seemed to be a highly skilled fighter as well. Like a ninja.

Eric, the largest of the group, could turn his body into living steel, possessing incredible strength and durability.

Nancy possessed the power to walk through solid objects, or allow them to pass through her with ease, yet not fall through the floor unless she wanted to.

Ginji possessed the ability to absorb and discharge electrical currents, like a living power plant.

Robin possessed the power to generate fire out of thin air, even directing it to other people and things with only a thought.

Sakura possessed the power to telekinetically move objects with only a thought. She could move dozens of smaller objects with ease. But the larger the object, the less number of objects she could manipulate.

Toga possessed superhuman speed, and not just the ability to run, but with his hands as well.

Shinji possessed his claws and ability to heal, but also heightened senses and enhanced strength as a result of his adamantium skeleton. He wasn't as strong as Eric, but still stronger than the others.

Iris was also able to enhance Rei's power to generate her AT-Field without strain on her body. Misato was somewhat shocked at this, finding out that Rei was part Angel, and again she had another reason to throttle Ritsuko, who apparently knew about that as well.

Since then the group had gotten to know each other better, telling stories of their lives, their exploits and adventures. But now it was almost noon and Misato came to the bones of the situation.

"So... what are you going to do now?" Misato asked as the group sat down in the living room, eating takeout.

"Our purpose was to come here and help Shinji." Iris said, still holding Jean-Paul.

"Does that mean you're staying... or taking Shinji with you?" she asked, somewhat fearfully.

"If he chooses to come with us, we would welcome him." the girl said.

"Shinji-kun is not going anywhere, without me!" Rei said, clutching Shinji's arm tightly.

Shinji just smiled as he stared at the blue-haired girl.

"I don't think that is going to be a...problem." Iris said as she suddenly felt her face go pale.

"Iris? What's wrong?" Sakura asked.

"Everyone Down!" she shouted as a figure exploded through the glass doors of Misato's balcony.

The group took cover, diving away and covering their faces from the shower of glass as a lithe red and black garbed figure, obviously female and equipt with numerous weapons all over her body stepped into the room.

Everyone looked at her as she grinned beneath her mask.

"My name is Deadpool, and I'm here to kill Shinji Ikari." the red and black figure said.

"I'm Shinji Ikari." the brown-haired boy said, standing up and unsheathing his claws.

"Goody! I'm your new instructor in pain, so let's get this session underway!" she shouted as she pulled her swords from her back and leapt at the boy.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

Author's Notes:

Next time on 'Shinji X', Shinji vs Asuka in a brawl that everyone has been waiting for.

Hope no one minds, but I've been busy with trying to update my stories, and this one has been on the back burner for a long time now. I just only recently got back to it.

Hope it meets with everyone's standards. Also, I've got something special planned for Gendo.

Hint, hint, it has to do with another one of Wolverine's enemies. His most feral one.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

OMAKE!

Iris teleported herself into the bedroom of Shinji Ikari and Rei Ayanami, only to find the pair fully naked and in a compromising position.

"Oh my!" she gasped, covering the eyes of her bear. "My Virgin Eyes!" she shouted as she teleported out.

"Who was that?" Shinji asked, looking up at Rei's naked body.

"I do not know, but she made me lose my rhythm!" Rei huffed as she sat naked on top of Shinji.

HHHHHHHHHHHHHHHHHHHHHHHHHHH

OMAKE 2

"I can't believe you convinced them to do this." Ritsuko groaned as the young group of mutant heroes were cleaning her apartment.

Ginji was using his electrical powers to power the vacuum cleaner to suck up the dirt and dust.

Naruto was using his duplication powers to gather up the trash.

Eric was hauling out the mounds of trash that Naruto was collecting.

Nancy was using her phasing powers to get the better angles at cleaning the bathtub and shower and under the sinks.

Robin was using her powers to incinerate the more disgusting pieces of Misato's trash.

Sakura was levitating the clothes around the room so as to wash them, not wanting to touch the piles of human filth.

Toga was out on a grocery store run, several in fact.

As for Shinji... he was trying to kill the living cooking experiment that Misato had created and all but forgot about in the fridge.

"I wonder... would they be willing to clean mine when they are done?" Ritsuko asked.

"I can give you a good rate." Iris said to the blond doctor.


End file.
